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- PDB-7nvj: Crystal structure of UFC1 Y110A & F121A -

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Basic information

Entry
Database: PDB / ID: 7nvj
TitleCrystal structure of UFC1 Y110A & F121A
ComponentsUbiquitin-fold modifier-conjugating enzyme 1
KeywordsLIGASE / Ubiquitin fold conjugating enzyme 1 (UFC1) / Ufmylation / Y110A / F121A
Function / homology
Function and homology information


UFM1 conjugating enzyme activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome
Similarity search - Function
Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-fold modifier-conjugating enzyme 1 / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-fold modifier-conjugating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsManoj Kumar, P. / Padala, P. / Isupov, M.N. / Wiener, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1383/17 Israel
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for UFM1 transfer from UBA5 to UFC1.
Authors: Kumar, M. / Padala, P. / Fahoum, J. / Hassouna, F. / Tsaban, T. / Zoltsman, G. / Banerjee, S. / Cohen-Kfir, E. / Dessau, M. / Rosenzweig, R. / Isupov, M.N. / Schueler-Furman, O. / Wiener, R.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin-fold modifier-conjugating enzyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5593
Polymers19,3751
Non-polymers1842
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-0 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.161, 46.161, 143.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1


Mass: 19375.254 Da / Num. of mol.: 1 / Mutation: Y110A, F121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Plasmid: pET32A / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q9Y3C8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→33.24 Å / Num. obs: 8491 / % possible obs: 99.8 % / Redundancy: 1.2 % / Biso Wilson estimate: 25.44 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.153 / Net I/σ(I): 13.33
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 804 / CC1/2: 0.47 / Rrim(I) all: 0.71 / % possible all: 99.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z6P

2z6p


Resolution: 2.2→33.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.2 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.246 444 5.229 %Random selection
Rwork0.1928 8047 --
all0.196 ---
obs-8491 99.824 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.088 Å2-0 Å2-0 Å2
2--0.088 Å2-0 Å2
3----0.175 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 12 47 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131361
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171268
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.6451845
X-RAY DIFFRACTIONr_angle_other_deg1.2581.5782939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.445163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46922.39471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76315228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.327159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.2210.2293
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21206
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2643
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.250.215
X-RAY DIFFRACTIONr_nbd_other0.1750.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.28
X-RAY DIFFRACTIONr_mcbond_it2.2392.693655
X-RAY DIFFRACTIONr_mcbond_other2.2382.685654
X-RAY DIFFRACTIONr_mcangle_it3.5384.024817
X-RAY DIFFRACTIONr_mcangle_other3.5364.034818
X-RAY DIFFRACTIONr_scbond_it2.6482.987706
X-RAY DIFFRACTIONr_scbond_other2.6462.988707
X-RAY DIFFRACTIONr_scangle_it4.1264.331028
X-RAY DIFFRACTIONr_scangle_other4.1244.3321029
X-RAY DIFFRACTIONr_lrange_it7.38550.3575929
X-RAY DIFFRACTIONr_lrange_other7.38250.3455921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.347340.2685510.2725910.7880.82698.98480.251
2.257-2.3190.327370.275700.2746090.7940.8499.67160.25
2.319-2.3860.275230.2465400.2485650.840.85999.6460.224
2.386-2.4590.278310.2375340.245660.8420.86799.82330.213
2.459-2.5390.332280.2265120.2315400.8330.8851000.202
2.539-2.6280.323200.2275090.235290.8590.8941000.193
2.628-2.7270.199310.2084960.2075270.9310.9111000.179
2.727-2.8380.254180.1964650.1994830.8980.931000.165
2.838-2.9630.305220.2144540.2174760.8770.921000.176
2.963-3.1070.29280.1824380.1884660.9020.9361000.155
3.107-3.2750.268250.1834150.1874400.8860.9411000.153
3.275-3.4720.302240.1653820.1724060.890.9541000.139
3.472-3.710.309200.1533670.1613880.9170.96399.74230.136
3.71-4.0050.177200.1453560.1473760.9640.9741000.134
4.005-4.3840.197240.1393200.1433440.960.9751000.129
4.384-4.8950.15110.1553100.1543210.9730.9721000.138
4.895-5.640.165210.1962640.1932850.9630.9621000.179
5.64-6.880.245140.2032390.2052530.9450.9541000.177
6.88-9.6130.186100.1911910.192010.9730.9591000.178
9.613-43.9510.22730.2191310.221360.9830.95898.52940.23

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